Here’s an interesting letter in the current issue of Nature Biotechnology (subscription only):
In the course of analyzing the evolution of the Blocks database2, we noticed errors in the software source code used to create the initial BLOSUM family of matrices [...] The result of these errors is that the BLOSUM matrices—BLOSUM62, BLOSUM50, etc.—are quite different from the matrices that should have been calculated using the algorithm described by Henikoff and Henikoff. Obviously, minor errors in research, and particularly in software source code, are quite common. This case is noteworthy for three reasons: first, the BLOSUM matrices are ubiquitous in computational biology; second, these errors have gone unnoticed for 15 years; and third, the ‘incorrect’ matrices perform better than the ‘intended’ matrices.
Are they right? Does it matter?